From 4c80f5f141b06a0939ced6b4945f7db7a6827308 Mon Sep 17 00:00:00 2001 From: Ivan Blagoev Topolsky Date: Fri, 31 May 2024 18:01:41 +0200 Subject: [PATCH] support frameshift_deletions_checks chain - use bfctools' --chain option instead of mafft --- workflow/rules/consensus.smk | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/workflow/rules/consensus.smk b/workflow/rules/consensus.smk index 8249d7e9..42dd7e36 100644 --- a/workflow/rules/consensus.smk +++ b/workflow/rules/consensus.smk @@ -184,8 +184,8 @@ rule frameshift_deletions_checks: input: REF_NAME=reference_file, BAM=alignment_wildcard, - #REF_majority_dels="{dataset}/references/ref_majority_dels.fasta", - REF_majority_dels="{dataset}/references/consensus.bcftools.fasta", + CONSENSUS="{dataset}/references/consensus.bcftools.fasta", + CHAIN="{dataset}/references/consensus.bcftools.chain", GENES_GFF=( cachepath(config.input["genes_gff"]) if config.input["genes_gff"] else [] ), @@ -207,7 +207,7 @@ rule frameshift_deletions_checks: threads: 1 shell: """ - {params.FRAMESHIFT_DEL_CHECKS} -i {input.BAM} -c {input.REF_majority_dels} -f {input.REF_NAME} -g {input.GENES_GFF} --english=true -o {output.FRAMESHIFT_DEL_CHECK_TSV} 2> >(tee {log.errfile} >&2) + {params.FRAMESHIFT_DEL_CHECKS} -i {input.BAM} -c {input.CONSENSUS} --chain {input.CHAIN} -f {input.REF_NAME} -g {input.GENES_GFF} --english=true -o {output.FRAMESHIFT_DEL_CHECK_TSV} 2> >(tee {log.errfile} >&2) """